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- PDB-5vu2: Electron cryo-microscopy of "immature" Chikungunya VLP -

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Basic information

Entry
Database: PDB / ID: 5vu2
TitleElectron cryo-microscopy of "immature" Chikungunya VLP
Components
  • (E1 envelope glycoprotein) x 2
  • E2 envelope glycoprotein
  • E3 envelope glycoprotein
  • capsid proteinCapsid
KeywordsVIRUS LIKE PARTICLE / Chikungunya / virus / immature
Function / homologyAlphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set ...Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Peptidase S3, togavirin / Togavirin / T=4 icosahedral viral capsid / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / Structural polyprotein / Structural polyprotein / Structural polyprotein
Function and homology information
Specimen sourceChikungunya virus strain Senegal 37997
Chikungunya virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.8 Å resolution
AuthorsRossmann, M.G. / Yap, M.L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural studies of Chikungunya virus maturation.
Authors: Moh Lan Yap / Thomas Klose / Akane Urakami / S Saif Hasan / Wataru Akahata / Michael G Rossmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 18, 2017 / Release: Dec 6, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 6, 2017Structure modelrepositoryInitial release
1.1Dec 20, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Jan 3, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)911,44424
Polyers911,44424
Non-polymers00
Water0
1
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 60


Theoretical massNumber of molelcules
Total (without water)54,686,6421440
Polyers54,686,6421440
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 5


  • icosahedral pentamer
  • 4.56 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)4,557,220120
Polyers4,557,220120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 6


  • icosahedral 23 hexamer
  • 5.47 MDa, 144 polymers
Theoretical massNumber of molelcules
Total (without water)5,468,664144
Polyers5,468,664144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide
E1 envelope glycoprotein


Mass: 95538.164 Da / Num. of mol.: 8 / Fragment: UNP residues 326-1191 / Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: A0A0H4CWF2
#2: Protein/peptide
E3 envelope glycoprotein


Mass: 6926.990 Da / Num. of mol.: 4 / Fragment: UNP residues 266-324 / Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Gene: CHIKVgp2 / Production host: Homo sapiens (human) / References: UniProt: C7S7A1, UniProt: Q5XXP3*PLUS
#3: Protein/peptide
capsid protein / Capsid


Mass: 16229.508 Da / Num. of mol.: 4 / Fragment: UNP residues 113-261 / Source: (gene. exp.) Chikungunya virus (strain 37997) / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
#4: Protein/peptide
E1 envelope glycoprotein


Mass: 4810.723 Da / Num. of mol.: 4 / Fragment: transmembrane helix (UNP residues 1203-1248) / Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
#5: Protein/peptide
E2 envelope glycoprotein


Mass: 8817.458 Da / Num. of mol.: 4 / Fragment: transmembrane helix (UNP residues 668-748) / Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chikungunya virus strain Senegal 37997 / Type: VIRUS / Entity ID: 1, 2, 3, 4, 5 / Source: RECOMBINANT
Source (natural)Organism: Chikungunya virus strain Senegal 37997
Source (recombinant)Cell: Human embryonic kidney / Organism: Homo sapiens (human) / Plasmid: pUC119
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
7EMfitmodel fitting
13jspr3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 72944 / Symmetry type: POINT

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